'ladder bands' in PCR - (Apr/25/2007 )

Sometimes in the late cycles of PCR amplification, the ends of the product strands anneal to each other faster than the primers can anneal to them. When this happens, you get a ladder of 2-, 4- 6- 8- and 10-strand complexes (decreasing in band intensity as they get more complex). Running these on a highly denaturing TBE/Urea gel will force them to run as the single-stranded form of the correct size.